2022/04/01

Today’s Schedule

Discussion about Scientific Writing and the Review Process led by Shanna and Nhi!

  • Sternberg, R.J. (1997). “Eight common misconceptions about psychology papers” in The Psychologist’s Companion: A Guide to Scientific Writing for Students and Researchers, 3rd Ed., 6-19. Cambridge University Press.
  • Wicker, A. W. (1985). Getting out of our conceptual ruts: Strategies for expanding conceptual frameworks. American Psychologist, 40(10), 1094-1103.
  • McGuire, W.J. (1997). Creative hypothesis generating in psychology: Some useful heuristics. Annual Review of Psychology, 48(1), 1–30.
  • Abelson, R.O. (1995). “Articulation of results: Ticks and buts”. In Statistics as Principled Argument, 1st Ed. Hillsdale, NJ: Lawrence Erlbaum, pp. 104-131.
  • Smith, R. (2006). Peer review: A flawed process at the heart of science and journals. Journal of the Royal Society of Medicine, 99(4), 178–182.

Supplemental: Meta-Analysis and Viz!

  • Cribbie-Meta_Analysis.pdf and Ex-MetaAnalysis.Rmd

library(ggplot2)
dat <- read.csv("exerciseDat.csv")

Box Plot

ggplot(dat, aes(x = group, y = score2)) + geom_boxplot() + 
    stat_summary(fun.y=mean, colour="red", size=5, geom="point")

Side-by-Side Histograms

ggplot(data = dat, aes(x = score2)) + geom_histogram(binwidth = 5) + 
  facet_wrap(facets = ~ group)

Overlapping Density Plot

ggplot(data = dat, aes(x = score2, colour = group)) + geom_density()

Violin Plot

Visualizing Proportions: Pie Charts

Visualizing Proportions: Waffle Plots

#install.packages("waffle")
library(waffle)
animals <- c(`Tigers (33)`= 33, 
             `Lions (29)`= 29, 
             `Zebras (19)`= 19,
             `Giraffes (10)` = 10,
             `Elephants (7)` = 7,
             `Other (2)` = 2)

waffle(animals, 
       title="What is your favourite animal?",
       rows = 5,
       legend_pos = "bottom")

Visualizing Proportions: Waffle Plots

library(vcdExtra)
data(Alligator, package = "vcdExtra")
head(Alligator) # TABLE FORM
##      lake  sex  size    food count
## 1 Hancock male small    fish     7
## 2 Hancock male small  invert     1
## 3 Hancock male small reptile     0
## 4 Hancock male small    bird     0
## 5 Hancock male small   other     5
## 6 Hancock male large    fish     4

names(Alligator)[5] <- "Freq"
Alligator.Full <- expand.dft(Alligator)
## Warning in type.convert.default(as.character(DF[[i]]), ...): 'as.is' should be
## specified by the caller; using TRUE

## Warning in type.convert.default(as.character(DF[[i]]), ...): 'as.is' should be
## specified by the caller; using TRUE

## Warning in type.convert.default(as.character(DF[[i]]), ...): 'as.is' should be
## specified by the caller; using TRUE

## Warning in type.convert.default(as.character(DF[[i]]), ...): 'as.is' should be
## specified by the caller; using TRUE
head(Alligator.Full)
##      lake  sex  size food
## 1 Hancock male small fish
## 2 Hancock male small fish
## 3 Hancock male small fish
## 4 Hancock male small fish
## 5 Hancock male small fish
## 6 Hancock male small fish

xcats <- xtabs(~food + size, data = Alligator.Full)
xcats
##          size
## food      large small
##   bird        8     5
##   fish       45    49
##   invert     16    45
##   other      13    19
##   reptile    13     6
chisq.test(xcats)
## 
##  Pearson's Chi-squared test
## 
## data:  xcats
## X-squared = 14.772, df = 4, p-value = 0.005198

library(vcd)
mosaic(xcats, shade=T) 

library(vcd)
fourfold(xtabs(~sex + size, data = Alligator.Full))

mosaic(xtabs(~size + food + sex, data=Alligator.Full), shade = TRUE)

Next Time on…

  • April 8th: Readings on “Replication and Reproducibility”

  • Tong, C. (2019) Statistical Inference Enables Bad Science; Statistical Thinking Enables Good Science. The American Statistician, 73(1), 246-261.

  • Schimmack, U. (2012). The Ironic Effect of Significant Results on the Credibility of Multiple-Study Articles. Psychological Methods, 17(4), 551-566.

  • Nosek, B.A. et al. (2015). Promoting an open research culture. Science, 348(6242), 1422–1425.

  • Open Science Collaboration (2015). Estimating the reproducibility of psychological science. Science, 349(6251), 943–943.

  • Spellman, B.A. (2015). A Short (Personal) Future History of Revolution 2.0. Perspectives on Psychological Science, 10(6), 886–899.